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        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.21

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/aquascope analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2024-11-02, 18:18 EDT based on data in: /scicomp/scratch/xuz1/nextflow/work/49/ff96f8827e7eccf0d8e9a233486c3e


        General Statistics

        Showing 2/2 rows and 2/2 columns.
        Sample NameTop lineageTop lineage %
        Sample1XBB.1.5* [Omicron (XBB.1.5.X)]
        76.8%
        Sample2XBB* (XBB.X)
        71.6%

        NWSS/aquascope Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.

        Methods

        Data was processed using NWSS/aquascope v3.0 (doi: ) of the nf-core collection of workflows (Ewels et al., 2020).

        The pipeline was executed with Nextflow v24.04.2 (Di Tommaso et al., 2017) with the following command:

        nextflow run main.nf --resume -profile singularity,test_bam -entry FREYJA_ONLY --outdir ~/projects/tmp/aqua//freyja

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        CDCGov-Aquascope Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        runName
        stupefied_keller
        containerEngine
        singularity
        launchDir
        /scicomp/home-pure/xuz1/projects/aqua/aquascope
        workDir
        /scicomp/scratch/xuz1/nextflow/work
        projectDir
        /scicomp/home-pure/xuz1/projects/aqua/aquascope
        userName
        xuz1
        profile
        singularity,test_bam
        configFiles
        N/A

        Input/output options

        input
        /scicomp/home-pure/xuz1/projects/aqua/aquascope/assets/samplesheet_test_bam.csv
        outdir
        ~/projects/tmp/aqua//freyja

        Institutional config options

        config_profile_name
        Test BAM input
        config_profile_description
        Minimal test dataset to check pipeline function

        Max job request options

        max_cpus
        2
        max_memory
        6 GB
        max_time
        6h

        Other parameters

        gff3
        /scicomp/home-pure/xuz1/projects/aqua/aquascope/assests/references/SARS-CoV-2.reference.gff3
        hostnames
        {}

        Freyja

        Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples.DOI: 10.1038/s41586-022-05049-6.

        Freyja Summary

        Relative lineage abundances from mixed SARS-CoV-2 samples. Hover over the column headers for descriptions and click Help for more in-depth documentation.

        The graph denotes a sum of all lineage abundances in a particular WHO designation , otherwise they are grouped into "Other". Lineages abundances are calculated as the number of reads that are assigned to a particular lineage. Lineages and their corresponding abundances are summarized by constellation.

        Note: Lineage designation is based on the used WHO nomenclature, which could vary over time.

        Created with MultiQC